A goal of plant breeding is to combine, in a single plant, various desirable traits. For field crops such as corn, these traits can include greater yield and better agronomic quality. However, genetic loci that influence yield and agronomic quality are not always known, and even if known, their contributions to such traits are frequently unclear.
Once discovered, however, desirable genetic loci can be selected for as part of a breeding program in order to generate plants that carry desirable traits. An exemplary approach for generating such plants includes the transfer by introgression of nucleic acid sequences from plants that have desirable genetic information into plants that do not by crossing the plants using traditional breeding techniques. Desirable loci can be introgressed into commercially available plant varieties using marker-assisted selection (MAS) or marker-assisted breeding (MAB). MAS and MAB involve the use of one or more of the molecular markers for the identification and selection of those plants that contain one or more loci that encode desired traits. Such identification and selection can be based on selection of informative markers that are associated with desired traits.
However, even when desirable genetic loci are known, the analysis of the genomes of plants that carry the desirable genetic loci can be extremely time-consuming. Not only do samples need to be isolated from plants, but the genomic contents of the samples must be isolated and analyzed, usually individually and in isolation from all other such samples. Successful application of a genome analysis system thus typically requires pure, high-quality genomic DNA (gDNA), and having a highly specific, reproducible, and efficient method for preparing the same with quickly and with low cost would be desirable. It would be further desirable if such a system could be automated or otherwise designed for high-throughput applications.
Additionally, such a system should preferably remove any and all inhibitors of downstream analytical techniques that might be introduced into the gDNA sample. Sources of such inhibitors can include the preparation reagents themselves as well as components of the plant tissues and/or cells that remain in the isolated gDNA sample. In particular, isolation of plant gDNA frequently results in the presence of high levels of polysaccharides, polyphenols, pigments, and/or other secondary metabolites (see Wen & Deng, 2002), the presence of which can make gDNA preparations unusable in downstream analyses (see Michiels et al., 2003; Qiang et al., 2004).